I found the problem, it is JavaScript. If you toggle it on and off while you are in the cockpit you can actually fly. It is difficult here this is what I did-
go to travel, yeah it goes away. But then go to your settings and turn JavaScript off,
go back to your cockpit hit refresh you're able to travel -
select destination and Hit go- it will then say you can't do this without JavaScript but it actually is going.
Go back to your settings turn JavaScript back on -
go back to your cockpit refresh - everything is working fine.

This issue is still unresolved. It turns out that the phone I was using to test this, I hadn't fully updated. =\

Either we will fix this issue or apple will. Sadly, given the way the stupid cockpit is set up, this isn't something that is going to be easy to fix. I will give it the attention it deserves, and hopefully this can be resolved soon, but we shall see...

Still problematic, - best advice so far - d/l Mini Opera browser, - it displays a second travel window and allows travel normally. It doesnt refresh automatically, but if noone finds a sollution to safari/ios 6 combo....

____________

Kai Arkanian
"Character is what you have left when you've lost everything"

So I have been able to pilot no problem but I just discovered that the same issue exists when in a mine trying to access materials. It flashes showing the NPC's and then goes blank exactly like it used to with piloting.
Has anyone else had this problem?

I'm using iPhone 5 with latest update and traveling is fine just input coordinates, problem for me is rest of pilot interface: cargo,scan, passengers, stats etc none work only get the blank screen where info should be after clicking. Really hope can be fixed somehow not filing ticket as already in bug base. Just adding what I was missing